Research on various aspects of Giardia lamblia is limited. Most studies are collaborative in nature. We have completed genomic sequencing of isolates GS( genotype B) and DH( genotype A2) and compared theme to a draft sequence of GS and the previously published sequence of WB. THe results show that GS is very different from WB and DH and strongly suggests it is a different species. Giardia lamblia (syn Giardia intestinalis, Giardia duodenalis) is the most common pathogenic intestinal parasite of humans worldwide and is a frequent cause of endemic and epidemic diarrhea and gastrointestinal upset. G. lamblia infects a wide range of mammals and humans but humans are almost always infected with genotypes A and B. G. lamblia isolates are composed of a group of related organisms or genotypes but little is known how they differ or the extent of their diversity and genomic coding differences. To unambiguously determine the relationship among genotypes, we sequenced to high depth coverage and accurately assembled the GS and DH (Genotypes B and A2) isolates and compared them to nearly completed chromosomal sequences of the WB genome and draft sequencing surveys of genotypes E (pig isolate) and B (GS; human isolate). We found that the genome of GS differs from WB-A1 and Pig-E more than previously realized. DH, the first genotype A2 isolate sequenced, is closely related to WB-A1 and appears to have the smallest sequenced genome for a Giardia isolate to date. While genome synteny exists between genotypes, recombination within and across chromosomes of the individual genotypes is evident. Our findings suggest that GS is a different species from the other genotypes, as supported by the degree of genomic diversity, coding capacity, heterozygosity, phylogenetic distance and known biological differences from WB-A1 and other G.lamblia genotypes